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Goloe D, Gildor T, Ben-Tabou de-Leon S. Expression and Transcriptional Targets of TGFβ-RII in Paracentrotus lividus Larval Skeletogenesis. Genesis 2024; 62:e23614. [PMID: 39139086 DOI: 10.1002/dvg.23614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024]
Abstract
Organisms from the five kingdoms of life use minerals to harden their tissues and make teeth, shells and skeletons, in the process of biomineralization. The sea urchin larval skeleton is an excellent system to study the biological regulation of biomineralization and its evolution. The gene regulatory network (GRN) that controls sea urchin skeletogenesis is known in great details and shows similarity to the GRN that controls vertebrates' vascularization while it is quite distinct from the GRN that drives vertebrates' bone formation. Yet, transforming growth factor beta (TGF-β) signaling regulates both sea urchin and vertebrates' skeletogenesis. Here, we study the upstream regulation and identify transcriptional targets of TGF-β in the Mediterranean Sea urchin species, Paracentrotus lividus. TGF-βRII is transiently active in the skeletogenic cells downstream of vascular endothelial growth factor (VEGF) signaling, in P. lividus. Continuous perturbation of TGF-βRII activity significantly impairs skeletal elongation and the expression of key skeletogenic genes. Perturbation of TGF-βRII after skeletal initiation leads to a delay in skeletal elongation and minor changes in gene expression. TGF-β targets are distinct from its transcriptional targets during vertebrates' bone formation, suggesting that the role of TGF-β in biomineralization in these two phyla results from convergent evolution.
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Affiliation(s)
- Daniel Goloe
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Tsvia Gildor
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Smadar Ben-Tabou de-Leon
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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2
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Larouche-Bilodeau C, Cameron CB. Acorn worm ossicle ultrastructure and composition and the origin of the echinoderm skeleton. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220773. [PMID: 36147942 PMCID: PMC9490348 DOI: 10.1098/rsos.220773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/31/2022] [Indexed: 05/02/2023]
Abstract
Here, we describe the shape and mineral composition of ossicles from eight acorn worm species, bringing the total known biomineralizing enteropneusts to 10 and confirming that ossicles are widespread in Enteropneusta. Three general forms were identified including a globular form that occurs in all three major enteropneust families. The biomineral compositions included all three polymorphs of calcium carbonate; calcite, aragonite and vaterite, and low to high magnesium concentrations. Calcite was the most common and characteristic of echinoderm ossicles. Based on these findings we hypothesize that an enteropneust-like ancestor to the Ambulacraria had ectodermal ossicles, formed in an extracellular occluded space bordered by a sheath of sclerocyte cells. The ossicles were microscopic, monotypic globular shaped, calcite ossicles with low to high Mg content and MSP130 proteins. The ossicles lacked intercalation with other ossicles. The function of acorn worm ossicles is unknown, but the position of ossicles in the trunk epithelia and near to the surface suggests predator deterrence, to provide grip on the walls of a burrow or tube, as storage of metabolic waste, or to regulate blood pH, rather than as an endoskeleton function seen in fossil and crown group Echinodermata.
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Affiliation(s)
| | - Christopher B. Cameron
- Département de sciences biologiques, University of Montreal, Montreal, Quebec, Canada H3C 3J7
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3
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Larouche-Bilodeau C, Cameron CB. Acorn worm ossicle ultrastructure and composition and the origin of the echinoderm skeleton. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220773. [PMID: 36147942 DOI: 10.5281/zenodo.5103051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/31/2022] [Indexed: 05/18/2023]
Abstract
Here, we describe the shape and mineral composition of ossicles from eight acorn worm species, bringing the total known biomineralizing enteropneusts to 10 and confirming that ossicles are widespread in Enteropneusta. Three general forms were identified including a globular form that occurs in all three major enteropneust families. The biomineral compositions included all three polymorphs of calcium carbonate; calcite, aragonite and vaterite, and low to high magnesium concentrations. Calcite was the most common and characteristic of echinoderm ossicles. Based on these findings we hypothesize that an enteropneust-like ancestor to the Ambulacraria had ectodermal ossicles, formed in an extracellular occluded space bordered by a sheath of sclerocyte cells. The ossicles were microscopic, monotypic globular shaped, calcite ossicles with low to high Mg content and MSP130 proteins. The ossicles lacked intercalation with other ossicles. The function of acorn worm ossicles is unknown, but the position of ossicles in the trunk epithelia and near to the surface suggests predator deterrence, to provide grip on the walls of a burrow or tube, as storage of metabolic waste, or to regulate blood pH, rather than as an endoskeleton function seen in fossil and crown group Echinodermata.
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Affiliation(s)
| | - Christopher B Cameron
- Département de sciences biologiques, University of Montreal, Montreal, Quebec, Canada H3C 3J7
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4
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Tarsis K, Gildor T, Morgulis M, Ben-Tabou de-Leon S. Distinct regulatory states control the elongation of individual skeletal rods in the sea urchin embryo. Dev Dyn 2022; 251:1322-1339. [PMID: 35403290 PMCID: PMC9543741 DOI: 10.1002/dvdy.474] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/28/2022] [Accepted: 04/06/2022] [Indexed: 11/09/2022] Open
Abstract
Background Understanding how gene regulatory networks (GRNs) control developmental progression is a key to the mechanistic understanding of morphogenesis. The sea urchin larval skeletogenesis provides an excellent platform to tackle this question. In the early stages of sea urchin skeletogenesis, skeletogenic genes are uniformly expressed in the skeletogenic lineage. Yet, during skeletal elongation, skeletogenic genes are expressed in distinct spatial sub‐domains. The regulation of differential gene expression during late skeletogenesis is not well understood. Results Here we reveal the dynamic expression of the skeletogenic regulatory genes that define a specific regulatory state for each pair of skeletal rods, in the sea urchin Paracentrotus lividus. The vascular endothelial growth factor (VEGF) signaling, essential for skeleton formation, specifically controls the migration of cells that form the postoral and distal anterolateral skeletogenic rods. VEGF signaling also controls the expression of regulatory genes in cells at the tips of the postoral rods, including the transcription factors Pitx1 and MyoD1. Pitx1 activity is required for normal skeletal elongation and for the expression of some of VEGF target genes. Conclusions Our study illuminates the fine‐tuning of the regulatory system during the transition from early to late skeletogenesis that gives rise to rod‐specific regulatory states. The skeletogenic transcription factors form specific regulatory states in various skeletogenic sub‐populations. Late VEGF signaling controls the regulatory states at the tips of the post‐oral and anterolateral skeletal rods. VEGF signaling controls the expression of the transcription factors, MyoD1 and Pitx1. Pitx1 activity is required for normal skeletal elongation and for the expression of some of VEGF target genes.
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Affiliation(s)
- Kristina Tarsis
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Tsvia Gildor
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Miri Morgulis
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Smadar Ben-Tabou de-Leon
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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5
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Epigenetic forest and flower morphogenesis. Comput Biol Chem 2022; 98:107667. [PMID: 35339093 DOI: 10.1016/j.compbiolchem.2022.107667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 02/14/2022] [Accepted: 03/16/2022] [Indexed: 11/21/2022]
Abstract
This paper studies the epigenetic process that leads to Angiosperms' flower architecture (flowering plants). As a case study, we analyze the flower Arabidopsis thaliana's GRN obtained during cell fate determination in the early stages of the flower's development, which was constructed in a previous work using experimental data. We start by constructing and analyzing the Epigenetic Forest, a discrete representation of Waddington's Epigenetic Landscape, obtained as the transition graph of the discrete dynamical system associated with the GRN. Next, we propose an optimization problem to model morphogenesis by defining a biologically meaningful function that accounts for the work involved in cell specialization. Finally, the problem is solved using a genetic algorithm. The optimal solution found by the algorithm correctly recovers the flower's architecture, as observed in wild type flowers and recovered in other theoretical works. Even though the case study addresses this specific problem, the method is directly applicable to other GRN's with attractors consisting of equilibrium points only and could be extended to the situation where there are periodic attractors.
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Khor JM, Ettensohn CA. Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene. eLife 2022; 11:72834. [PMID: 35212624 PMCID: PMC8903837 DOI: 10.7554/elife.72834] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
The gene regulatory network (GRN) that underlies echinoderm skeletogenesis is a prominent model of GRN architecture and evolution. KirrelL is an essential downstream effector gene in this network and encodes an Ig-superfamily protein required for the fusion of skeletogenic cells and the formation of the skeleton. In this study, we dissected the transcriptional control region of the kirrelL gene of the purple sea urchin, Strongylocentrotus purpuratus. Using plasmid- and bacterial artificial chromosome-based transgenic reporter assays, we identified key cis-regulatory elements (CREs) and transcription factor inputs that regulate Sp-kirrelL, including direct, positive inputs from two key transcription factors in the skeletogenic GRN, Alx1 and Ets1. We next identified kirrelL cis-regulatory regions from seven other echinoderm species that together represent all classes within the phylum. By introducing these heterologous regulatory regions into developing sea urchin embryos we provide evidence of their remarkable conservation across ~500 million years of evolution. We dissected in detail the kirrelL regulatory region of the sea star, Patiria miniata, and demonstrated that it also receives direct inputs from Alx1 and Ets1. Our findings identify kirrelL as a component of the ancestral echinoderm skeletogenic GRN. They support the view that GRN subcircuits, including specific transcription factor–CRE interactions, can remain stable over vast periods of evolutionary history. Lastly, our analysis of kirrelL establishes direct linkages between a developmental GRN and an effector gene that controls a key morphogenetic cell behavior, cell–cell fusion, providing a paradigm for extending the explanatory power of GRNs.
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Affiliation(s)
- Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States
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7
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Abstract
Larvae of sea urchins have a population of conspicuous pigmented cells embedded in the outer surface epithelium. Pigment cells are a distinct mesodermal lineage that gives rise to a key component of the larval immune system. During cleavage, signaling from adjacent cells influences a small crescent of cells to initiate a network of genetic interactions that prepare the cells for morphogenesis and specializes them as immunocytes. The cells become active during gastrulation, detach from the epithelium, migrate through the blastocoel, and insert into the ectoderm where they complete their differentiation. Studies of pigment cell development have helped establish how cellular signaling controls networks of genetic interactions that bring about morphogenesis and differentiation. This review summarizes studies of pigment cell development and concludes that pigment cells are an excellent experimental model. Pigment cells provide several opportunities to further test and refine our understanding of the molecular basis of cellular development.
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Affiliation(s)
- Robert D Burke
- Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
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8
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Su YH. Dorsal-ventral axis formation in sea urchin embryos. Curr Top Dev Biol 2022; 146:183-210. [PMID: 35152983 DOI: 10.1016/bs.ctdb.2021.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Most sea urchin species produce planktonic feeding larvae with distinct dorsal-ventral polarity. Such morphological indicators of polarity arise after gastrulation, when several morphogenesis and cell differentiation events occur differentially along the dorsal-ventral axis. For instance, the gut bends toward the ventral side where the mouth will form, skeletogenesis occurs initially near the ventral side with the forming skeleton extending dorsally, and pigment cells differentiate and embed in the dorsal ectoderm. The patterning mechanisms and gene regulatory networks underlying these events have been extensively studied. Two opposing TGF-β signaling pathways, Nodal and BMP, play key roles in all three germ layers to respectively pattern the sea urchin ventral and dorsal sides. In this chapter, I describe our current understanding of sea urchin dorsal-ventral patterning mechanisms. Additionally, differences in the patterning mechanisms observed in lecithotrophic sea urchins (nonfeeding larvae) and in cidaroid sea urchins are also discussed, along with evolutionary insights gained from comparative analyses.
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Affiliation(s)
- Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
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9
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Chang WL, Su YH. Zygotic hypoxia-inducible factor alpha regulates spicule elongation in the sea urchin embryo. Dev Biol 2022; 484:63-74. [DOI: 10.1016/j.ydbio.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 01/28/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
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Beatman TR, Buckley KM, Cary GA, Hinman VF, Ettensohn CA. A nomenclature for echinoderm genes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6350312. [PMID: 34386815 PMCID: PMC8361234 DOI: 10.1093/database/baab052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/02/2021] [Accepted: 08/02/2021] [Indexed: 12/16/2022]
Abstract
Echinoderm embryos and larvae are prominent experimental model systems for studying developmental mechanisms. High-quality, assembled, annotated genome sequences are now available for several echinoderm species, including representatives from most classes. The increased availability of these data necessitates the development of a nomenclature that assigns universally interpretable gene symbols to echinoderm genes to facilitate cross-species comparisons of gene functions, both within echinoderms and across other phyla. This paper describes the implementation of an improved set of echinoderm gene nomenclature guidelines that both communicates meaningful orthology information in protein-coding gene symbols and names and establishes continuity with nomenclatures developed for major vertebrate model organisms, including humans. Differences between the echinoderm gene nomenclature guidelines and vertebrate guidelines are examined and explained. This nomenclature incorporates novel solutions to allow for several types of orthologous relationships, including the single echinoderm genes with multiple vertebrate co-orthologs that result from whole-genome-duplication events. The current version of the Echinoderm Gene Nomenclature Guidelines can be found at https://www.echinobase.org/gene/static/geneNomenclature.jsp Database URL https://www.echinobase.org/
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Affiliation(s)
- Thomas R Beatman
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.,Echinobase, #646 Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, USA
| | - Katherine M Buckley
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences, Auburn, AL 36849, USA
| | - Gregory A Cary
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.,Echinobase, #646 Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.,Echinobase, #646 Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, USA
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11
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Biodiversity-based development and evolution: the emerging research systems in model and non-model organisms. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1236-1280. [PMID: 33893979 DOI: 10.1007/s11427-020-1915-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/16/2021] [Indexed: 02/07/2023]
Abstract
Evolutionary developmental biology, or Evo-Devo for short, has become an established field that, broadly speaking, seeks to understand how changes in development drive major transitions and innovation in organismal evolution. It does so via integrating the principles and methods of many subdisciplines of biology. Although we have gained unprecedented knowledge from the studies on model organisms in the past decades, many fundamental and crucially essential processes remain a mystery. Considering the tremendous biodiversity of our planet, the current model organisms seem insufficient for us to understand the evolutionary and physiological processes of life and its adaptation to exterior environments. The currently increasing genomic data and the recently available gene-editing tools make it possible to extend our studies to non-model organisms. In this review, we review the recent work on the regulatory signaling of developmental and regeneration processes, environmental adaptation, and evolutionary mechanisms using both the existing model animals such as zebrafish and Drosophila, and the emerging nonstandard model organisms including amphioxus, ascidian, ciliates, single-celled phytoplankton, and marine nematode. In addition, the challenging questions and new directions in these systems are outlined as well.
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12
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Morgulis M, Winter MR, Shternhell L, Gildor T, Ben-Tabou de-Leon S. VEGF signaling activates the matrix metalloproteinases, MmpL7 and MmpL5 at the sites of active skeletal growth and MmpL7 regulates skeletal elongation. Dev Biol 2021; 473:80-89. [PMID: 33577829 DOI: 10.1016/j.ydbio.2021.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/20/2022]
Abstract
Organisms can uptake minerals, shape them in different forms and generate teeth, skeletons or shells that support and protect them. Mineral uptake, trafficking and nucleation are tightly regulated by the biomineralizing cells through networks of specialized proteins. Specifically, matrix metalloproteases (MMPs) digest various extracellular substrates and allow for mineralization in the vertebrates' teeth and bones, but little is known about their role in invertebrates' systems. The sea urchin embryo provides an excellent invertebrate model for genetic and molecular studies of biomineralization. MMP inhibition prevents the growth of the calcite spicules of the sea urchin larval skeleton, however, the molecular mechanisms and genes that underlie this response are not well understood. Here we study the spatial expression and regulation of two membrane type MMPs that were found to be occluded in the sea urchin spicules, Pl-MmpL7 and Pl-MmpL5, and investigate the function of Pl-MmpL7 in skeletogenesis. The inhibition of MMPs does not change the volume of the calcium vesicles in the skeletogenic cells. The expression of Pl-MmpL7 and Pl-MmpL5 is regulated by the Vascular Endothelial Growth Factor (VEGF) signaling, from the time of skeleton initiation and on. The expression of these genes is localized to the subsets of skeletogenic cells where active spicule growth occurs throughout skeletogenesis. Downregulation of Pl-MmpL7 expression delays the growth of the skeletal rods and in some cases, strongly perturbs skeletal shape. The localized expression of Pl-MmpL7 and Pl-MmpL5 to the active growth zone and the effect of Pl-MmpL7 perturbations on skeletal growth, suggest that these genes are essential for normal spicule elongation in the sea urchin embryo.
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Affiliation(s)
- Miri Morgulis
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel
| | - Mark R Winter
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel
| | - Ligal Shternhell
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel
| | - Tsvia Gildor
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel
| | - Smadar Ben-Tabou de-Leon
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel.
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13
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Kipryushina YO, Yakovlev KV. Maternal control of early patterning in sea urchin embryos. Differentiation 2020; 113:28-37. [PMID: 32371341 DOI: 10.1016/j.diff.2020.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023]
Abstract
Sea urchin development has been studied extensively for more than a century and considered regulative since the first experimental evidence. Further investigations have repeatedly supported this standpoint by revealing the presence of inductive mechanisms that alter cell fate decisions at early cleavage stages and flexibility of development in response to environmental conditions. Some features indicate that sea urchin development is not completely regulative, but actually includes determinative events. In 16-cell embryos, mesomeres and macromeres represent multipotency, while the cell fate of most vegetal micromeres is restricted. It is known that the mature sea urchin eggs are polarized by the asymmetrical distribution of some maternal mRNAs and proteins. Spatially-distributed maternal factors are necessary for the orientation of the primary animal-vegetal axis, which is established by both maternal and zygotic mechanisms later in development. The secondary dorsal-ventral axis is conditionally specified later in development. Dorsal-ventral polarity is very liable during the early cleavages, though more recent data argue that its direction may be oriented by maternal asymmetry. In this review, we focus on the role of maternal factors in initial embryonic patterning during the first cleavages of sea urchin embryos before activation of the embryonic genome.
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Affiliation(s)
- Yulia O Kipryushina
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Palchevsky St. 17, 690041, Vladivostok, Russia
| | - Konstantin V Yakovlev
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Palchevsky St. 17, 690041, Vladivostok, Russia; Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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14
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Ettensohn CA. The gene regulatory control of sea urchin gastrulation. Mech Dev 2020; 162:103599. [PMID: 32119908 DOI: 10.1016/j.mod.2020.103599] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 02/07/2023]
Abstract
The cell behaviors associated with gastrulation in sea urchins have been well described. More recently, considerable progress has been made in elucidating gene regulatory networks (GRNs) that underlie the specification of early embryonic territories in this experimental model. This review integrates information from these two avenues of work. I discuss the principal cell movements that take place during sea urchin gastrulation, with an emphasis on molecular effectors of the movements, and summarize our current understanding of the gene regulatory circuitry upstream of those effectors. A case is made that GRN biology can provide a causal explanation of gastrulation, although additional analysis is needed at several levels of biological organization in order to provide a deeper understanding of this complex morphogenetic process.
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Affiliation(s)
- Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA.
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15
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Kostyun JL, Gibson MJS, King CM, Moyle LC. A simple genetic architecture and low constraint allow rapid floral evolution in a diverse and recently radiating plant genus. THE NEW PHYTOLOGIST 2019; 223:1009-1022. [PMID: 30972773 DOI: 10.1111/nph.15844] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Genetic correlations among different components of phenotypes, especially those resulting from pleiotropy, can constrain or facilitate trait evolution. These factors could especially influence the evolution of traits that are functionally integrated, such as those comprising the flower. Indeed, pleiotropy is proposed as a main driver of repeated convergent trait transitions, including the evolution of phenotypically similar pollinator syndromes. We assessed the role of pleiotropy in the differentiation of floral and other reproductive traits between two species - Jaltomata sinuosa and J. umbellata (Solanaceae) - that have divergent suites of floral traits consistent with bee and hummingbird pollination, respectively. To do so, we generated a hybrid population and examined the genetic architecture (trait segregation and quantitative trait locus (QTL) distribution) underlying 25 floral and fertility traits. We found that most floral traits had a relatively simple genetic basis (few, predominantly additive, QTLs of moderate to large effect), as well as little evidence of antagonistic pleiotropy (few trait correlations and QTL colocalization, particularly between traits of different classes). However, we did detect a potential case of adaptive pleiotropy among floral size and nectar traits. These mechanisms may have facilitated the rapid floral trait evolution observed within Jaltomata, and may be a common component of rapid phenotypic change more broadly.
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Affiliation(s)
- Jamie L Kostyun
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
- Department of Plant Biology, The University of Vermont, Burlington, VT, 05405, USA
| | | | - Christian M King
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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16
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Moreno B, DiCorato A, Park A, Mobilia K, Knapp R, Bleher R, Wilke C, Alvares K, Joester D. Culture of and experiments with sea urchin embryo primary mesenchyme cells. Methods Cell Biol 2019; 150:293-330. [PMID: 30777181 PMCID: PMC8273911 DOI: 10.1016/bs.mcb.2019.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Skeletogenesis in the sea urchin embryo gives rise to a pair of intricate endoskeletal spicules. Deposition of these skeletal elements in the early larva is the outcome of a morphogenetic program that begins with maternal inputs in the early zygote and results in the specification of the large micromere-primary mesenchyme cell (PMC) lineage. PMCs are of considerable interest as a model system, not only to dissect the mechanism of specific developmental processes, but also to investigate their evolution and the unrivaled level of control over the formation of a graded, mechanically robust, yet single crystalline biomineral. The ability to study gene regulatory circuits, cellular behavior, signaling pathways, and molecular players involved in biomineralization is significantly boosted by the high level of autonomy of PMCs. In fact, in the presence of horse serum, micromeres differentiate into PMCs and produce spicules in vitro, separated from the embryonic milieu. PMC culture eliminates indirect effects that can complicate the interpretation of experiments in vivo, offers superior spatiotemporal control, enables PMC-specific readouts, and is compatible with most imaging and characterization techniques. In this chapter, we provide an updated protocol, based on the pioneering work by Okazaki and Wilt, for the isolation of micromeres and subsequent culture of PMCs, as well as protocols for fixation and staining for fluorescent microscopy, preparation of cell cultures for electron microscopy, and the isolation of RNA.
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Affiliation(s)
- Bradley Moreno
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Allessandra DiCorato
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Alexander Park
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Kellen Mobilia
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Regina Knapp
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Reiner Bleher
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Charlene Wilke
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Keith Alvares
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Derk Joester
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States.
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17
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Shashikant T, Khor JM, Ettensohn CA. From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms. Genesis 2018; 56:e23253. [PMID: 30264451 PMCID: PMC6294693 DOI: 10.1002/dvg.23253] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/14/2018] [Accepted: 09/23/2018] [Indexed: 01/19/2023]
Abstract
The skeletogenic gene regulatory network (GRN) of sea urchins and other echinoderms is one of the most intensively studied transcriptional networks in any developing organism. As such, it serves as a preeminent model of GRN architecture and evolution. This review summarizes our current understanding of this developmental network. We describe in detail the most comprehensive model of the skeletogenic GRN, one developed for the euechinoid sea urchin Strongylocentrotus purpuratus, including its initial deployment by maternal inputs, its elaboration and stabilization through regulatory gene interactions, and its control of downstream effector genes that directly drive skeletal morphogenesis. We highlight recent comparative studies that have leveraged the euechinoid GRN model to examine the evolution of skeletogenic programs in diverse echinoderms, studies that have revealed both conserved and divergent features of skeletogenesis within the phylum. Last, we summarize the major insights that have emerged from analysis of the structure and evolution of the echinoderm skeletogenic GRN and identify key, unresolved questions as a guide for future work.
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Affiliation(s)
- Tanvi Shashikant
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
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18
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Sepúlveda-Ramírez SP, Toledo-Jacobo L, Henson JH, Shuster CB. Cdc42 controls primary mesenchyme cell morphogenesis in the sea urchin embryo. Dev Biol 2018; 437:140-151. [PMID: 29555242 PMCID: PMC5973877 DOI: 10.1016/j.ydbio.2018.03.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 03/05/2018] [Accepted: 03/15/2018] [Indexed: 12/15/2022]
Abstract
In the sea urchin embryo, gastrulation is characterized by the ingression and directed cell migration of primary mesenchyme cells (PMCs), as well as the primary invagination and convergent extension of the endomesoderm. Like all cell shape changes, individual and collective cell motility is orchestrated by Rho family GTPases and their modulation of the actomyosin cytoskeleton. And while endomesoderm specification has been intensively studied in echinoids, much less is known about the proximate regulators driving cell motility. Toward these ends, we employed anti-sense morpholinos, mutant alleles and pharmacological inhibitors to assess the role of Cdc42 during sea urchin gastrulation. While inhibition of Cdc42 expression or activity had only mild effects on PMC ingression, PMC migration, alignment and skeletogenesis were disrupted in the absence of Cdc42, as well as elongation of the archenteron. PMC migration and patterning of the larval skeleton relies on the extension of filopodia, and Cdc42 was required for filopodia in vivo as well as in cultured PMCs. Lastly, filopodial extension required both Arp2/3 and formin actin-nucleating factors, supporting models of filopodial nucleation observed in other systems. Together, these results suggest that Cdc42 plays essential roles during PMC cell motility and organogenesis.
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Affiliation(s)
- Silvia P Sepúlveda-Ramírez
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, United States; University of Washington Friday Harbor Laboratories, Friday Harbor, WA 98250, United States
| | - Leslie Toledo-Jacobo
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, United States; University of Washington Friday Harbor Laboratories, Friday Harbor, WA 98250, United States
| | - John H Henson
- University of Washington Friday Harbor Laboratories, Friday Harbor, WA 98250, United States; Department of Biology, Dickinson College, Carlisle, PA 17013, United States
| | - Charles B Shuster
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, United States; University of Washington Friday Harbor Laboratories, Friday Harbor, WA 98250, United States.
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19
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Cvekl A, Zhao Y, McGreal R, Xie Q, Gu X, Zheng D. Evolutionary Origins of Pax6 Control of Crystallin Genes. Genome Biol Evol 2018; 9:2075-2092. [PMID: 28903537 PMCID: PMC5737492 DOI: 10.1093/gbe/evx153] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2017] [Indexed: 12/19/2022] Open
Abstract
The birth of novel genes, including their cell-specific transcriptional control, is a major source of evolutionary innovation. The lens-preferred proteins, crystallins (vertebrates: α- and β/γ-crystallins), provide a gateway to study eye evolution. Diversity of crystallins was thought to originate from convergent evolution through multiple, independent formation of Pax6/PaxB-binding sites within the promoters of genes able to act as crystallins. Here, we propose that αB-crystallin arose from a duplication of small heat shock protein (Hspb1-like) gene accompanied by Pax6-site and heat shock element (HSE) formation, followed by another duplication to generate the αA-crystallin gene in which HSE was converted into another Pax6-binding site. The founding β/γ-crystallin gene arose from the ancestral Hspb1-like gene promoter inserted into a Ca2+-binding protein coding region, early in the cephalochordate/tunicate lineage. Likewise, an ancestral aldehyde dehydrogenase (Aldh) gene, through multiple gene duplications, expanded into a multigene family, with specific genes expressed in invertebrate lenses (Ω-crystallin/Aldh1a9) and both vertebrate lenses (η-crystallin/Aldh1a7 and Aldh3a1) and corneas (Aldh3a1). Collectively, the present data reconstruct the evolution of diverse crystallin gene families.
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Affiliation(s)
- Ales Cvekl
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York.,Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Yilin Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Rebecca McGreal
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York.,Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Qing Xie
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York.,Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Xun Gu
- Program in Bioinformatics and Computational Biology, Department of Genetics, Development, and Cell Biology, Iowa State University
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York.,Department of Neurology, Albert Einstein College of Medicine, Bronx, New York.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York
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20
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Shashikant T, Khor JM, Ettensohn CA. Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling. BMC Genomics 2018; 19:206. [PMID: 29558892 PMCID: PMC5859501 DOI: 10.1186/s12864-018-4542-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/13/2018] [Indexed: 12/11/2022] Open
Abstract
Background The developmental gene regulatory network (GRN) that underlies skeletogenesis in sea urchins and other echinoderms is a paradigm of GRN structure, function, and evolution. This transcriptional network is deployed selectively in skeleton-forming primary mesenchyme cells (PMCs) of the early embryo. To advance our understanding of this model developmental GRN, we used genome-wide chromatin accessibility profiling to identify and characterize PMC cis-regulatory modules (CRMs). Results ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) analysis of purified PMCs provided a global picture of chromatin accessibility in these cells. We used both ATAC-seq and DNase-seq (DNase I hypersensitive site sequencing) to identify > 3000 sites that exhibited increased accessibility in PMCs relative to other embryonic cell lineages, and provide both computational and experimental evidence that a large fraction of these sites represent bona fide skeletogenic CRMs. Putative PMC CRMs were preferentially located near genes differentially expressed by PMCs and consensus binding sites for two key transcription factors in the PMC GRN, Alx1 and Ets1, were enriched in these CRMs. Moreover, a high proportion of candidate CRMs drove reporter gene expression specifically in PMCs in transgenic embryos. Surprisingly, we found that PMC CRMs were partially open in other embryonic lineages and exhibited hyperaccessibility as early as the 128-cell stage. Conclusions Our work provides a comprehensive picture of chromatin accessibility in an early embryonic cell lineage. By identifying thousands of candidate PMC CRMs, we significantly enhance the utility of the sea urchin skeletogenic network as a general model of GRN architecture and evolution. Our work also shows that differential chromatin accessibility, which has been used for the high-throughput identification of enhancers in differentiated cell types, is a powerful approach for the identification of CRMs in early embryonic cells. Lastly, we conclude that in the sea urchin embryo, CRMs that control the cell type-specific expression of effector genes are hyperaccessible several hours in advance of gene activation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4542-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tanvi Shashikant
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
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21
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Liang J, Li J, Fu Y, Ren F, Xu J, Zhou M, Li P, Feng H, Wang Y. GdX/UBL4A null mice exhibit mild kyphosis and scoliosis accompanied by dysregulation of osteoblastogenesis and chondrogenesis. Cell Biochem Funct 2018; 36:129-136. [DOI: 10.1002/cbf.3324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 12/27/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Jiao Liang
- State Key Laboratory of Membrane Biology, School of Medicine; Tsinghua University; Beijing China
| | - Jun Li
- State Key Laboratory of Membrane Biology, School of Medicine; Tsinghua University; Beijing China
| | - Yanxia Fu
- State Key Laboratory of Membrane Biology, School of Medicine; Tsinghua University; Beijing China
- Tsinghua University-Perking University Joint Center for Life Sciences; Beijing China
| | - Fangli Ren
- State Key Laboratory of Membrane Biology, School of Medicine; Tsinghua University; Beijing China
| | - Jiake Xu
- School of Biomedical Sciences; University of Western Australia; Perth Western Australia Australia
| | - Mengyu Zhou
- Department of Dentistry; The First Affiliated Hospital of Guangxi Medical University; Nanning China
| | - Peiyu Li
- The General Hospital of the People's Liberation Army; Beijing China
| | - Haotian Feng
- Research Centre for Regenerative Medicine; Guangxi Medical University; Nanning China
| | - Yinyin Wang
- State Key Laboratory of Membrane Biology, School of Medicine; Tsinghua University; Beijing China
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22
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Khor JM, Ettensohn CA. Functional divergence of paralogous transcription factors supported the evolution of biomineralization in echinoderms. eLife 2017; 6:e32728. [PMID: 29154754 PMCID: PMC5758115 DOI: 10.7554/elife.32728] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/16/2017] [Indexed: 12/12/2022] Open
Abstract
Alx1 is a pivotal transcription factor in a gene regulatory network that controls skeletogenesis throughout the echinoderm phylum. We performed a structure-function analysis of sea urchin Alx1 using a rescue assay and identified a novel, conserved motif (Domain 2) essential for skeletogenic function. The paralogue of Alx1, Alx4, was not functionally interchangeable with Alx1, but insertion of Domain 2 conferred robust skeletogenic function on Alx4. We used cross-species expression experiments to show that Alx1 proteins from distantly related echinoderms are not interchangeable, although the sequence and function of Domain 2 are highly conserved. We also found that Domain 2 is subject to alternative splicing and provide evidence that this domain was originally gained through exonization. Our findings show that a gene duplication event permitted the functional specialization of a transcription factor through changes in exon-intron organization and thereby supported the evolution of a major morphological novelty.
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Affiliation(s)
- Jian Ming Khor
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghUnited States
| | - Charles A Ettensohn
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghUnited States
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23
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Cavalieri V, Geraci F, Spinelli G. Diversification of spatiotemporal expression and copy number variation of the echinoid hbox12/pmar1/micro1 multigene family. PLoS One 2017; 12:e0174404. [PMID: 28350855 PMCID: PMC5370098 DOI: 10.1371/journal.pone.0174404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 03/08/2017] [Indexed: 11/26/2022] Open
Abstract
Changes occurring during evolution in the cis-regulatory landscapes of individual members of multigene families might impart diversification in their spatiotemporal expression and function. The archetypal member of the echinoid hbox12/pmar1/micro1 family is hbox12-a, a homeobox-containing gene expressed exclusively by dorsal blastomeres, where it governs the dorsal/ventral gene regulatory network during embryogenesis of the sea urchin Paracentrotus lividus. Here we describe the inventory of the hbox12/pmar1/micro1 genes in P. lividus, highlighting that gene copy number variation occurs across individual sea urchins of the same species. We show that the various hbox12/pmar1/micro1 genes group into three subfamilies according to their spatiotemporal expression, which ranges from broad transcription throughout development to transient expression in either the animal hemisphere or micromeres of the early embryo. Interestingly, the promoter regions of those genes showing comparable expression patterns are highly similar, while differing from those of the other subfamilies. Strikingly, phylogenetic analysis suggests that the hbox12/pmar1/micro1 genes are species-specific, exhibiting extensive divergence in their noncoding, but not in their coding, sequences across three distinct sea urchin species. In spite of this, two micromere-specific genes of P. lividus possess a TCF/LEF-binding motif in a similar position, and their transcription relies on Wnt/β-catenin signaling, similar to the pmar1 and micro1 genes, which in other sea urchin species are involved in micromere specification. Altogether, our findings suggest that the hbox12/pmar1/micro1 gene family evolved rather rapidly, generating paralogs whose cis-regulatory sequences diverged following multiple rounds of duplication from a common ancestor.
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Affiliation(s)
- Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Edificio 16, Palermo, Italy
- Advanced Technologies Network Center (ATeN), University of Palermo, Viale delle Scienze Edificio 18, Palermo, Italy
- * E-mail: (VC); (GS)
| | - Fabiana Geraci
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Edificio 16, Palermo, Italy
| | - Giovanni Spinelli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Edificio 16, Palermo, Italy
- * E-mail: (VC); (GS)
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24
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Stepicheva NA, Dumas M, Kobi P, Donaldson JG, Song JL. The small GTPase Arf6 regulates sea urchin morphogenesis. Differentiation 2017; 95:31-43. [PMID: 28188999 DOI: 10.1016/j.diff.2017.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 12/08/2016] [Accepted: 01/26/2017] [Indexed: 12/31/2022]
Abstract
The small GTPase Arf6 is a conserved protein that is expressed in all metazoans. Arf6 remodels cytoskeletal actin and mediates membrane protein trafficking between the plasma membrane in its active form and endosomal compartments in its inactive form. While a rich knowledge exists for the cellular functions of Arf6, relatively little is known about its physiological role in development. This study examines the function of Arf6 in mediating cellular morphogenesis in early development. We dissect the function of Arf6 with a loss-of-function morpholino and constitutively active Arf6-Q67L construct. We focus on the two cell types that undergo active directed migration: the primary mesenchyme cells (PMCs) that give rise to the sea urchin skeleton and endodermal cells that form the gut. Our results indicate that Arf6 plays an important role in skeleton formation and PMC migration, in part due to its ability to remodel actin. We also found that embryos injected with Arf6 morpholino have gastrulation defects and embryos injected with constitutively active Arf6 have endodermal cells detached from the gut epithelium with decreased junctional cadherin staining, indicating that Arf6 may mediate the recycling of cadherin. Thus, Arf6 impacts cells that undergo coordinated movement to form embryonic structures in the developing embryo.
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Affiliation(s)
- Nadezda A Stepicheva
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, United States
| | - Megan Dumas
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, United States
| | - Priscilla Kobi
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, United States
| | - Julie G Donaldson
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, United States.
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25
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Sun Z, Ettensohn CA. TGF-β sensu stricto signaling regulates skeletal morphogenesis in the sea urchin embryo. Dev Biol 2016; 421:149-160. [PMID: 27955944 DOI: 10.1016/j.ydbio.2016.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/05/2016] [Accepted: 12/05/2016] [Indexed: 10/20/2022]
Abstract
Cell-cell signaling plays a prominent role in the formation of the embryonic skeleton of sea urchins, but the mechanisms are poorly understood. In the present study, we uncover an essential role for TGF-β sensu stricto signaling in this process. We show that TgfbrtII, a type II receptor dedicated to signaling through TGF-β sensu stricto, is expressed selectively in skeletogenic primary mesenchyme cells (PMCs) during skeleton formation. Morpholino (MO) knockdowns and studies with a specific TgfbrtII inhibitor (ITD-1) in both S. purpuratus and Lytechinus variegatus embryos show that this receptor is required for biomineral deposition. We provide pharmacological evidence that Alk4/5/7 is the cognate TGF-β type I receptor that pairs with TgfbrtII and show by inhibitor treatments of isolated micromeres cultured in vitro that both Alk4/5/7 and TgfbrtII function cell-autonomously in PMCs. Gene expression and gene knockdown studies suggest that TGF-β sensu stricto may be the ligand that interacts with TgfbrtII and support the view that this TGF-β superfamily ligand provides an essential, permissive cue for skeletogenesis, although it is unlikely to provide spatial patterning information. Taken together, our findings reveal that this model morphogenetic process involves an even more diverse suite of cell signaling pathways than previously appreciated and show that PMCs integrate a complex set of both generalized and spatially localized cues in assembling the endoskeleton.
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Affiliation(s)
- Zhongling Sun
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, United States
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, United States.
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26
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Ettensohn CA, Dey D. KirrelL, a member of the Ig-domain superfamily of adhesion proteins, is essential for fusion of primary mesenchyme cells in the sea urchin embryo. Dev Biol 2016; 421:258-270. [PMID: 27866905 DOI: 10.1016/j.ydbio.2016.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/01/2016] [Accepted: 11/01/2016] [Indexed: 11/25/2022]
Abstract
In the sea urchin embryo, primary mesenchyme cells (PMCs) adhere to one another and fuse via filopodia, forming cable-like structures within which skeletal rods are deposited. Although this process was first described more than a century ago, molecules that participate in PMC adhesion and fusion have not been identified. Here we show that KirrelL, a PMC-specific, Ig domain-containing transmembrane protein, is essential for PMC fusion, probably by mediating filopodial adhesions that are a pre-requisite for subsequent membrane fusion. We show that KirrelL is not required for PMC specification, migration, or for direct filopodial contacts between PMCs. In the absence of KirrelL, however, filopodial contacts do not result in fusion. kirrelL is a member of a family of closely related, intronless genes that likely arose through an echinoid-specific gene expansion, possibly via retrotransposition. Our findings are significant in that they establish a direct linkage between the transcriptional network deployed in the PMC lineage and an effector molecule required for a critically important PMC morphogenetic process. In addition, our results point to a conserved role for Ig domain-containing adhesion proteins in facilitating cell fusion in both muscle and non-muscle cell lineages during animal development.
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Affiliation(s)
- Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, United States.
| | - Debleena Dey
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, United States
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27
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Navarrete IA, Levine M. Nodal and FGF coordinate ascidian neural tube morphogenesis. Development 2016; 143:4665-4675. [PMID: 27827820 DOI: 10.1242/dev.144733] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/21/2016] [Indexed: 01/06/2023]
Abstract
Formation of the vertebrate neural tube represents one of the premier examples of morphogenesis in animal development. Here, we investigate this process in the simple chordate Ciona intestinalis Previous studies have implicated Nodal and FGF signals in the specification of lateral and ventral neural progenitors. We show that these signals also control the detailed cellular behaviors underlying morphogenesis of the neural tube. Live-imaging experiments show that FGF controls the intercalary movements of ventral neural progenitors, whereas Nodal is essential for the characteristic stacking behavior of lateral cells. Ectopic activation of FGF signaling is sufficient to induce intercalary behaviors in cells that have not received Nodal. In the absence of FGF and Nodal, neural progenitors exhibit a default behavior of sequential cell divisions, and fail to undergo the intercalary and stacking behaviors essential for normal morphogenesis. Thus, cell specification events occurring prior to completion of gastrulation coordinate the morphogenetic movements underlying the organization of the neural tube.
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Affiliation(s)
- Ignacio A Navarrete
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, University of California, Berkeley, CA 94720, USA
| | - Michael Levine
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, University of California, Berkeley, CA 94720, USA
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28
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Martik ML, Lyons DC, McClay DR. Developmental gene regulatory networks in sea urchins and what we can learn from them. F1000Res 2016; 5. [PMID: 26962438 PMCID: PMC4765714 DOI: 10.12688/f1000research.7381.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/19/2016] [Indexed: 12/21/2022] Open
Abstract
Sea urchin embryos begin zygotic transcription shortly after the egg is fertilized. Throughout the cleavage stages a series of transcription factors are activated and, along with signaling through a number of pathways, at least 15 different cell types are specified by the beginning of gastrulation. Experimentally, perturbation of contributing transcription factors, signals and receptors and their molecular consequences enabled the assembly of an extensive gene regulatory network model. That effort, pioneered and led by Eric Davidson and his laboratory, with many additional insights provided by other laboratories, provided the sea urchin community with a valuable resource. Here we describe the approaches used to enable the assembly of an advanced gene regulatory network model describing molecular diversification during early development. We then provide examples to show how a relatively advanced authenticated network can be used as a tool for discovery of how diverse developmental mechanisms are controlled and work.
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Affiliation(s)
- Megan L Martik
- Biology Department, Duke University, Durham, North Carolina, 27708, USA
| | - Deirdre C Lyons
- Biology Department, Duke University, Durham, North Carolina, 27708, USA
| | - David R McClay
- Biology Department, Duke University, Durham, North Carolina, 27708, USA
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29
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Koga H, Fujitani H, Morino Y, Miyamoto N, Tsuchimoto J, Shibata TF, Nozawa M, Shigenobu S, Ogura A, Tachibana K, Kiyomoto M, Amemiya S, Wada H. Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton. PLoS One 2016; 11:e0149067. [PMID: 26866800 PMCID: PMC4750990 DOI: 10.1371/journal.pone.0149067] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/27/2016] [Indexed: 11/19/2022] Open
Abstract
Over the course of evolution, the acquisition of novel structures has ultimately led to wide variation in morphology among extant multicellular organisms. Thus, the origins of genetic systems for new morphological structures are a subject of great interest in evolutionary biology. The larval skeleton is a novel structure acquired in some echinoderm lineages via the activation of the adult skeletogenic machinery. Previously, VEGF signaling was suggested to have played an important role in the acquisition of the larval skeleton. In the present study, we compared expression patterns of Alx genes among echinoderm classes to further explore the factors involved in the acquisition of a larval skeleton. We found that the alx1 gene, originally described as crucial for sea urchin skeletogenesis, may have also played an essential role in the evolution of the larval skeleton. Unlike those echinoderms that have a larval skeleton, we found that alx1 of starfish was barely expressed in early larvae that have no skeleton. When alx1 overexpression was induced via injection of alx1 mRNA into starfish eggs, the expression patterns of certain genes, including those possibly involved in skeletogenesis, were altered. This suggested that a portion of the skeletogenic program was induced solely by alx1. However, we observed no obvious external phenotype or skeleton. We concluded that alx1 was necessary but not sufficient for the acquisition of the larval skeleton, which, in fact, requires several genetic events. Based on these results, we discuss how the larval expression of alx1 contributed to the acquisition of the larval skeleton in the putative ancestral lineage of echinoderms.
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Affiliation(s)
- Hiroyuki Koga
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Haruka Fujitani
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yoshiaki Morino
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Norio Miyamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Jun Tsuchimoto
- Division of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
- Institute for Molecular Science of Medicine, Aichi Medical University, Nagakute, Japan
| | | | - Masafumi Nozawa
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
- Department of Genetics, The Graduate University for Advanced Studies, Mishima, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Atsushi Ogura
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Kazunori Tachibana
- Graduate School of Bioscience, Tokyo Institute of Technology, Yokohama, Japan
| | - Masato Kiyomoto
- Marine and Coastal Research Center, Ochanomizu University, Tateyama, Japan
| | - Shonan Amemiya
- Marine and Coastal Research Center, Ochanomizu University, Tateyama, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Research and Education Center of Natural Sciences, Keio University, Yokohama, Japan
| | - Hiroshi Wada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Erkenbrack EM, Ako-Asare K, Miller E, Tekelenburg S, Thompson JR, Romano L. Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms. Dev Genes Evol 2016; 226:37-45. [PMID: 26781941 DOI: 10.1007/s00427-015-0527-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/29/2015] [Indexed: 10/22/2022]
Abstract
Diverse sampling of organisms across the five major classes in the phylum Echinodermata is beginning to reveal much about the structure and function of gene regulatory networks (GRNs) in development and evolution. Sea urchins are the most studied clade within this phylum, and recent work suggests there has been dramatic rewiring at the top of the skeletogenic GRN along the lineage leading to extant members of the euechinoid sea urchins. Such rewiring likely accounts for some of the observed developmental differences between the two major subclasses of sea urchins-cidaroids and euechinoids. To address effects of topmost rewiring on downstream GRN events, we cloned four downstream regulatory genes within the skeletogenic GRN and surveyed their spatiotemporal expression patterns in the cidaroid Eucidaris tribuloides. We performed phylogenetic analyses with homologs from other non-vertebrate deuterostomes and characterized their spatiotemporal expression by quantitative polymerase chain reaction (qPCR) and whole-mount in situ hybridization (WMISH). Our data suggest the erg-hex-tgif subcircuit, a putative GRN kernel, exhibits a mesoderm-specific expression pattern early in Eucidaris development that is directly downstream of the initial mesodermal GRN circuitry. Comparative analysis of the expression of this subcircuit in four echinoderm taxa allowed robust ancestral state reconstruction, supporting hypotheses that its ancestral function was to stabilize the mesodermal regulatory state and that it has been co-opted and deployed as a unit in mesodermal subdomains in distantly diverged echinoderms. Importantly, our study supports the notion that GRN kernels exhibit structural and functional modularity, locking down and stabilizing clade-specific, embryonic regulatory states.
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Affiliation(s)
- Eric M Erkenbrack
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Kayla Ako-Asare
- Department of Biology, Denison University, Granville, OH, 43023, USA
| | - Emily Miller
- Department of Biology, Denison University, Granville, OH, 43023, USA
| | - Saira Tekelenburg
- Department of Biology, Denison University, Granville, OH, 43023, USA
| | - Jeffrey R Thompson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Laura Romano
- Department of Biology, Denison University, Granville, OH, 43023, USA
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31
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Cavalieri V, Spinelli G. Ectopic hbox12 Expression Evoked by Histone Deacetylase Inhibition Disrupts Axial Specification of the Sea Urchin Embryo. PLoS One 2015; 10:e0143860. [PMID: 26618749 PMCID: PMC4664418 DOI: 10.1371/journal.pone.0143860] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/09/2015] [Indexed: 12/26/2022] Open
Abstract
Dorsal/ventral patterning of the sea urchin embryo depends upon the establishment of a Nodal-expressing ventral organizer. Recently, we showed that spatial positioning of this organizer relies on the dorsal-specific transcription of the Hbox12 repressor. Building on these findings, we determined the influence of the epigenetic milieu on the expression of hbox12 and nodal genes. We find that Trichostatin-A, a potent and selective histone-deacetylases inhibitor, induces histone hyperacetylation in hbox12 chromatin, evoking broad ectopic expression of the gene. Transcription of nodal concomitantly drops, prejudicing dorsal/ventral polarity of the resulting larvae. Remarkably, impairing hbox12 function, either in a spatially-restricted sector or in the whole embryo, specifically rescues nodal transcription in Trichostatin-A-treated larvae. Beyond strengthen the notion that nodal expression is not allowed in the presence of functional Hbox12 in the same cells, these results highlight a critical role of histone deacetylases in regulating the spatial expression of hbox12.
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Affiliation(s)
- Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Italy
- Mediterranean Center for Human Health Advanced Biotechnologies (CHAB), University of Palermo, Italy
- * E-mail: (VC); (GS)
| | - Giovanni Spinelli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Italy
- * E-mail: (VC); (GS)
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32
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Reinardy HC, Emerson CE, Manley JM, Bodnar AG. Tissue regeneration and biomineralization in sea urchins: role of Notch signaling and presence of stem cell markers. PLoS One 2015; 10:e0133860. [PMID: 26267358 PMCID: PMC4534296 DOI: 10.1371/journal.pone.0133860] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/02/2015] [Indexed: 11/30/2022] Open
Abstract
Echinoderms represent a phylum with exceptional regenerative capabilities that can reconstruct both external appendages and internal organs. Mechanistic understanding of the cellular pathways involved in regeneration in these animals has been hampered by the limited genomic tools and limited ability to manipulate regenerative processes. We present a functional assay to investigate mechanisms of tissue regeneration and biomineralization by measuring the regrowth of amputated tube feet (sensory and motor appendages) and spines in the sea urchin, Lytechinus variegatus. The ability to manipulate regeneration was demonstrated by concentration-dependent inhibition of regrowth of spines and tube feet by treatment with the mitotic inhibitor, vincristine. Treatment with the gamma-secretase inhibitor DAPT resulted in a concentration-dependent inhibition of regrowth, indicating that both tube feet and spine regeneration require functional Notch signaling. Stem cell markers (Piwi and Vasa) were expressed in tube feet and spine tissue, and Vasa-positive cells were localized throughout the epidermis of tube feet by immunohistochemistry, suggesting the existence of multipotent progenitor cells in these highly regenerative appendages. The presence of Vasa protein in other somatic tissues (e.g. esophagus, radial nerve, and a sub-population of coelomocytes) suggests that multipotent cells are present throughout adult sea urchins and may contribute to normal homeostasis in addition to regeneration. Mechanistic insight into the cellular pathways governing the tremendous regenerative capacity of echinoderms may reveal processes that can be modulated for regenerative therapies, shed light on the evolution of regeneration, and enable the ability to predict how these processes will respond to changing environmental conditions.
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Affiliation(s)
- Helena C. Reinardy
- Molecular Discovery Laboratory, Bermuda Institute of Ocean Sciences, St. George’s GE 01, Bermuda
| | - Chloe E. Emerson
- Molecular Discovery Laboratory, Bermuda Institute of Ocean Sciences, St. George’s GE 01, Bermuda
| | - Jason M. Manley
- Molecular Discovery Laboratory, Bermuda Institute of Ocean Sciences, St. George’s GE 01, Bermuda
| | - Andrea G. Bodnar
- Molecular Discovery Laboratory, Bermuda Institute of Ocean Sciences, St. George’s GE 01, Bermuda
- * E-mail:
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33
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Yamazaki A, Minokawa T. Expession patterns of mesenchyme specification genes in two distantly related echinoids, Glyptocidaris crenularis and Echinocardium cordatum. Gene Expr Patterns 2015; 17:87-97. [PMID: 25801498 DOI: 10.1016/j.gep.2015.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/13/2015] [Accepted: 03/14/2015] [Indexed: 10/23/2022]
Abstract
The molecular mechanism of the larval mesenchyme cell specification in echinoids has been well analyzed. However, most of the data have been provided by studies of a single group of echinoids, the order Camarodonta. Little is known about this mechanism in other echinoid orders. We examined the expression patterns of mesenchyme specification genes, micro1, hesC, alx1, tbr, ets1, cyp1, and gcm, in the two non-Camarodonta echinoids, Glyptocidaris crenularis and Echinocardium cordatum. We found that the expression patterns of some genes contained characteristics that were unique to one of the species; others were shared by the two species. Some of the shared characteristics of G. crenularis and E. cordatum are not found in the species belonging to Camarodonta, suggesting the derived status of this order. The expression of ets1 in E. cordatum aboral ectoderm is one of the molecular level modifications possibly related to an evolutionarily novel larval structure, the posterior process. Our results suggest that a considerable number of modifications in the mesenchyme specification mechanisms have been introduced during the echinoid evolution.
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Affiliation(s)
- Atsuko Yamazaki
- Research Center for Marine Biology, Graduate School of Life Sciences, Tohoku University, 9 Sakamoto, Asamushi, Aomori, Aomori 039-3501, Japan
| | - Takuya Minokawa
- Research Center for Marine Biology, Graduate School of Life Sciences, Tohoku University, 9 Sakamoto, Asamushi, Aomori, Aomori 039-3501, Japan.
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34
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Willaredt MA, Schlüter T, Nothwang HG. The gene regulatory networks underlying formation of the auditory hindbrain. Cell Mol Life Sci 2015; 72:519-535. [PMID: 25332098 PMCID: PMC11113740 DOI: 10.1007/s00018-014-1759-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/24/2014] [Accepted: 10/09/2014] [Indexed: 01/28/2023]
Abstract
Development and evolution of auditory hindbrain nuclei are two major unsolved issues in hearing research. Recent characterization of transgenic mice identified the rhombomeric origins of mammalian auditory nuclei and unraveled genes involved in their formation. Here, we provide an overview on these data by assembling them into rhombomere-specific gene regulatory networks (GRNs), as they underlie developmental and evolutionary processes. To explore evolutionary mechanisms, we compare the GRNs operating in the mammalian auditory hindbrain with data available from the inner ear and other vertebrate groups. Finally, we propose that the availability of genomic sequences from all major vertebrate taxa and novel genetic techniques for non-model organisms provide an unprecedented opportunity to investigate development and evolution of the auditory hindbrain by comparative molecular approaches. The dissection of the molecular mechanisms leading to auditory structures will also provide an important framework for auditory processing disorders, a clinical problem difficult to tackle so far. These data will, therefore, foster basic and clinical hearing research alike.
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Affiliation(s)
- Marc A Willaredt
- Neurogenetics group, Center of Excellence Hearing4All, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111, Oldenburg, Germany.
| | - Tina Schlüter
- Neurogenetics group, Center of Excellence Hearing4All, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111, Oldenburg, Germany
| | - Hans Gerd Nothwang
- Neurogenetics group, Center of Excellence Hearing4All, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111, Oldenburg, Germany.
- Research Center for Neurosensory Science, Carl von Ossietzky University Oldenburg, 26111, Oldenburg, Germany.
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35
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Signal-dependent regulation of the sea urchin skeletogenic gene regulatory network. Gene Expr Patterns 2014; 16:93-103. [PMID: 25460514 DOI: 10.1016/j.gep.2014.10.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 11/23/2022]
Abstract
The endoskeleton of the sea urchin embryo is produced by primary mesenchyme cells (PMCs). Maternal inputs activate a complex gene regulatory network (GRN) in the PMC lineage in a cell-autonomous fashion during early development, initially creating a uniform population of prospective skeleton-forming cells. Previous studies showed that at post-blastula stages of development, several effector genes in the network exhibit non-uniform patterns of expression, suggesting that their regulation becomes subject to local, extrinsic cues. Other studies have identified the VEGF and MAPK pathways as regulators of PMC migration, gene expression, and biomineralization. In this study, we used whole mount in situ hybridization (WMISH) to examine the spatial expression patterns of 39 PMC-specific/enriched mRNAs in Strongylocentrotus purpuratus embryos at the late gastrula, early prism and pluteus stages. We found that all 39 mRNAs (including several regulatory genes) showed non-uniform patterns of expression within the PMC syncytium, revealing a global shift in the regulation of the skeletogenic GRN from a cell-autonomous to a signal-dependent mode. In general, localized regions of elevated gene expression corresponded to sites of rapid biomineral deposition. We used a VEGFR inhibitor (axitinib) and a MEK inhibitor (U0126) to show that VEGF signaling and the MAPK pathway are essential for maintaining high levels of gene expression in PMCs at the tips of rods that extend from the ventral region of the embryo. These inhibitors affected gene expression in the PMCs in similar ways, suggesting that VEGF acts via the MAPK pathway. In contrast, axitinib and U0126 did not affect the localized expression of genes in PMCs at the tips of the body rods, which form on the dorsal side of the embryo. Our results therefore indicate that multiple signaling pathways regulate the skeletogenic GRN during late stages of embryogenesis-VEGF/MAPK signaling on the ventral side and a separate, unidentified pathway on the dorsal side. These two signaling pathways appear to be activated sequentially (ventral followed by dorsal) and many effector genes are subject to regulation by both pathways.
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36
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Becker JD, Takeda S, Borges F, Dolan L, Feijó JA. Transcriptional profiling of Arabidopsis root hairs and pollen defines an apical cell growth signature. BMC PLANT BIOLOGY 2014; 14:197. [PMID: 25080170 PMCID: PMC4236730 DOI: 10.1186/s12870-014-0197-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 07/14/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Current views on the control of cell development are anchored on the notion that phenotypes are defined by networks of transcriptional activity. The large amounts of information brought about by transcriptomics should allow the definition of these networks through the analysis of cell-specific transcriptional signatures. Here we test this principle by applying an analogue to comparative anatomy at the cellular level, searching for conserved transcriptional signatures, or conserved small gene-regulatory networks (GRNs) on root hairs (RH) and pollen tubes (PT), two filamentous apical growing cells that are a striking example of conservation of structure and function in plants. RESULTS We developed a new method for isolation of growing and mature root hair cells, analysed their transcriptome by microarray analysis, and further compared it with pollen and other single cell transcriptomics data. Principal component analysis shows a statistical relation between the datasets of RHs and PTs which is suggestive of a common transcriptional profile pattern for the apical growing cells in a plant, with overlapping profiles and clear similarities at the level of small GTPases, vesicle-mediated transport and various specific metabolic responses. Furthermore, cis-regulatory element analysis of co-regulated genes between RHs and PTs revealed conserved binding sequences that are likely required for the expression of genes comprising the apical signature. This included a significant occurrence of motifs associated to a defined transcriptional response upon anaerobiosis. CONCLUSIONS Our results suggest that maintaining apical growth mechanisms synchronized with energy yielding might require a combinatorial network of transcriptional regulation. We propose that this study should constitute the foundation for further genetic and physiological dissection of the mechanisms underlying apical growth of plant cells.
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Affiliation(s)
- Jörg D Becker
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Seiji Takeda
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
- Present address: Cell and Genome Biology, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kitaina-Yazuma Oji 74, Seika-cho, Soraku-gun, Kyoto 619-0244, Japan
| | - Filipe Borges
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- Present address: Cold Spring Harbor Laboratory, Cold Spring Harbor 11724, NY, USA
| | - Liam Dolan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - José A Feijó
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- Department of Cell Biology and Molecular Genetics, University of Maryland, 0118 BioScience Research Bldg, College Park 20742-5815, MD, USA
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37
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Ettensohn CA. Horizontal transfer of themsp130gene supported the evolution of metazoan biomineralization. Evol Dev 2014; 16:139-48. [DOI: 10.1111/ede.12074] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Charles A. Ettensohn
- Department of Biological Sciences; Carnegie Mellon University; 4400 Fifth Avenue Pittsburgh PA 15213 USA
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38
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Rafiq K, Shashikant T, McManus CJ, Ettensohn CA. Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins. Development 2014; 141:950-61. [PMID: 24496631 DOI: 10.1242/dev.105585] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A central challenge of developmental and evolutionary biology is to understand the transformation of genetic information into morphology. Elucidating the connections between genes and anatomy will require model morphogenetic processes that are amenable to detailed analysis of cell/tissue behaviors and to systems-level approaches to gene regulation. The formation of the calcified endoskeleton of the sea urchin embryo is a valuable experimental system for developing such an integrated view of the genomic regulatory control of morphogenesis. A transcriptional gene regulatory network (GRN) that underlies the specification of skeletogenic cells (primary mesenchyme cells, or PMCs) has recently been elucidated. In this study, we carried out a genome-wide analysis of mRNAs encoded by effector genes in the network and uncovered transcriptional inputs into many of these genes. We used RNA-seq to identify >400 transcripts differentially expressed by PMCs during gastrulation, when these cells undergo a striking sequence of behaviors that drives skeletal morphogenesis. Our analysis expanded by almost an order of magnitude the number of known (and candidate) downstream effectors that directly mediate skeletal morphogenesis. We carried out genome-wide analysis of (1) functional targets of Ets1 and Alx1, two pivotal, early transcription factors in the PMC GRN, and (2) functional targets of MAPK signaling, a pathway that plays an essential role in PMC specification. These studies identified transcriptional inputs into >200 PMC effector genes. Our work establishes a framework for understanding the genomic regulatory control of a major morphogenetic process and has important implications for reconstructing the evolution of biomineralization in metazoans.
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Affiliation(s)
- Kiran Rafiq
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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39
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Adomako-Ankomah A, Ettensohn CA. Growth factors and early mesoderm morphogenesis: insights from the sea urchin embryo. Genesis 2014; 52:158-72. [PMID: 24515750 DOI: 10.1002/dvg.22746] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 01/24/2014] [Accepted: 02/05/2014] [Indexed: 12/16/2022]
Abstract
The early morphogenesis of the mesoderm is critically important in establishing the body plan of the embryo. Recent research has led to a better understanding of the mechanisms that underlie this process, and growth factor signaling pathways have emerged as key regulators of the directional movements of mesoderm cells during gastrulation. In this review, we undertake a comparative analysis of the various essential functions of growth factor signaling pathways in regulating early mesoderm morphogenesis, with an emphasis on recent advances in the sea urchin embryo. We focus on the roles of the vascular endothelial growth factor (VEGF) and fibroblast growth factor (FGF) pathways in the migration of primary mesenchyme cells and the formation of the embryonic endoskeleton. We compare the functions of VEGF and FGF in sea urchins with the roles that these and other growth factors play in regulating mesoderm migration during gastrulation in Drosophila and vertebrates.
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40
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Christiaen L. Cis-regulatory timers for developmental gene expression. PLoS Biol 2013; 11:e1001698. [PMID: 24204213 PMCID: PMC3812112 DOI: 10.1371/journal.pbio.1001698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
How does a fertilized egg decode its own genome to eventually develop into a mature animal? Each developing cell must activate a battery of genes in a timely manner and according to the function it will ultimately perform, but how? During development of the notochord—a structure akin to the vertebrate spine—in a simple marine invertebrate, an essential protein called Brachyury binds to specific sites in its target genes. A study just published in PLOS Biology reports that if the target gene contains multiple Brachyury-binding sites it will be activated early in development but if it contains only one site it will be activated later. Genes that contain no binding site can still be activated by Brachyury, but only indirectly by an earlier Brachyury-dependent gene product, so later than the directly activated genes. Thus, this study shows how several genes can interpret the presence of a single factor differently to become active at distinct times in development.
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Affiliation(s)
- Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, College of Arts and Sciences, New York University, New York, New York, United States of America
- * E-mail:
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41
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Ferg M, Armant O, Yang L, Dickmeis T, Rastegar S, Strähle U. Gene transcription in the zebrafish embryo: regulators and networks. Brief Funct Genomics 2013; 13:131-43. [PMID: 24152666 DOI: 10.1093/bfgp/elt044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The precise spatial and temporal control of gene expression is a key process in the development, maintenance and regeneration of the vertebrate body. A substantial proportion of vertebrate genomes encode genes that control the transcription of the genetic information into mRNA. The zebrafish is particularly well suited to investigate gene regulatory networks underlying the control of gene expression during development due to the external development of its transparent embryos and the increasingly sophisticated tools for genetic manipulation available for this model system. We review here recent data on the analysis of cis-regulatory modules, transcriptional regulators and their integration into gene regulatory networks in the zebrafish, using the developing spinal cord as example.
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Affiliation(s)
- Marco Ferg
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany.
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42
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Adomako-Ankomah A, Ettensohn CA. Growth factor-mediated mesodermal cell guidance and skeletogenesis during sea urchin gastrulation. Development 2013; 140:4214-25. [PMID: 24026121 DOI: 10.1242/dev.100479] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Growth factor signaling pathways provide essential cues to mesoderm cells during gastrulation in many metazoans. Recent studies have implicated the VEGF and FGF pathways in providing guidance and differentiation cues to primary mesenchyme cells (PMCs) during sea urchin gastrulation, although the relative contributions of these pathways and the cell behaviors they regulate are not fully understood. Here, we show that FGF and VEGF ligands are expressed in distinct domains in the embryonic ectoderm of Lytechinus variegatus. We find that PMC guidance is specifically disrupted in Lv-vegf3 morphants and these embryos fail to form skeletal elements. By contrast, PMC migration is unaffected in Lv-fgfa morphants, and well-patterned but shortened skeletal elements form. We use a VEGFR inhibitor, axitinib, to show that VEGF signaling is essential not only for the initial phase of PMC migration (subequatorial ring formation), but also for the second phase (migration towards the animal pole). VEGF signaling is not required, however, for PMC fusion. Inhibition of VEGF signaling after the completion of PMC migration causes significant defects in skeletogenesis, selectively blocking the elongation of skeletal rods that support the larval arms, but not rods that form in the dorsal region of the embryo. Nanostring nCounter analysis of ∼100 genes in the PMC gene regulatory network shows a decrease in the expression of many genes with proven or predicted roles in biomineralization in vegf3 morphants. Our studies lead to a better understanding of the roles played by growth factors in sea urchin gastrulation and skeletogenesis.
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